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Detailed information for vg0907974545:

Variant ID: vg0907974545 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7974545
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GCATTTCCCACATTCATATTGATGTTAATGAATCTAGACATATATATCTATTTAGATTCATTAACATCAACATAAATGTGTGAAATGCTAGAATGATTTA[T/C]
ATTGTGAAACGGAGGAAGTACTATATATCTTATACTTGAATATACATATATAGGATGTGTTTATGTGTGTGATGACTGCCAGAGCATGCATGCATGTAAC

Reverse complement sequence

GTTACATGCATGCATGCTCTGGCAGTCATCACACACATAAACACATCCTATATATGTATATTCAAGTATAAGATATATAGTACTTCCTCCGTTTCACAAT[A/G]
TAAATCATTCTAGCATTTCACACATTTATGTTGATGTTAATGAATCTAAATAGATATATATGTCTAGATTCATTAACATCAATATGAATGTGGGAAATGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.40%	18.30%	0.34%	0.00%	NA
All Indica	2759	94.70%	5.30%	0.00%	0.00%	NA
All Japonica	1512	52.60%	46.40%	0.99%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	90.10%	9.90%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	90.70%	9.30%	0.00%	0.00%	NA
Temperate Japonica	767	38.30%	59.80%	1.83%	0.00%	NA
Tropical Japonica	504	79.60%	20.40%	0.00%	0.00%	NA
Japonica Intermediate	241	41.90%	57.70%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	17.80%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907974545	T -> C	LOC_Os09g13650-LOC_Os09g13660	intergenic_region ; MODIFIER	silent_mutation	Average:57.314; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907974545	NA	1.71E-08	mr1002	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	2.21E-10	mr1002	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	6.87E-06	mr1559	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	6.95E-06	NA	mr1586	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	5.05E-12	mr1002_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	8.70E-11	mr1002_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	2.35E-06	mr1011_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	1.38E-08	mr1330_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	4.07E-09	mr1378_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	1.10E-08	mr1379_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	9.56E-06	mr1409_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	9.21E-07	9.20E-07	mr1548_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	1.95E-07	mr1559_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	8.06E-08	mr1709_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0907974545	NA	9.25E-09	mr1805_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251